4UMF | pdb_00004umf

Crystal structure of 3-deoxy-D-manno-octulosonate 8-phosphate phosphatase from Moraxella catarrhalis in complex with Magnesium ion, Phosphate ion and KDO molecule

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
D	d4umfd_	Alpha and beta proteins (a/b)	HAD-like	HAD-like	automated matches	automated matches	(Moraxella catarrhalis BC8 ) [TaxId: 857574 ],	SCOPe (2.08)
C	d4umfc1	Alpha and beta proteins (a/b)	HAD-like	HAD-like	automated matches	automated matches	(Moraxella catarrhalis BC8 ) [TaxId: 857574 ],	SCOPe (2.08)
C	d4umfc2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Moraxella catarrhalis BC8 ) [TaxId: 857574 ],	SCOPe (2.08)
B	d4umfb_	Alpha and beta proteins (a/b)	HAD-like	HAD-like	automated matches	automated matches	(Moraxella catarrhalis BC8 ) [TaxId: 857574 ],	SCOPe (2.08)
A	d4umfa_	Alpha and beta proteins (a/b)	HAD-like	HAD-like	automated matches	automated matches	(Moraxella catarrhalis BC8 ) [TaxId: 857574 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D	SCOP2B Superfamily	HAD-like	8081284	3001890	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	HAD-like	8081284	3001890	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	HAD-like	8081284	3001890	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	HAD-like	8081284	3001890	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
D	Hydrolase_3	e4umfD1	A: a/b three-layered sandwiches	X: HAD domain-like	H: HAD domain-related	T: HAD-like	F: Hydrolase_3	ECOD (1.6)
C	Hydrolase_3	e4umfC1	A: a/b three-layered sandwiches	X: HAD domain-like	H: HAD domain-related	T: HAD-like	F: Hydrolase_3	ECOD (1.6)
B	Hydrolase_3	e4umfB1	A: a/b three-layered sandwiches	X: HAD domain-like	H: HAD domain-related	T: HAD-like	F: Hydrolase_3	ECOD (1.6)
A	Hydrolase_3	e4umfA1	A: a/b three-layered sandwiches	X: HAD domain-like	H: HAD domain-related	T: HAD-like	F: Hydrolase_3	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	3.40.50.1000	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	HAD superfamily/HAD-like	CATH (4.3.0)
C	3.40.50.1000	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	HAD superfamily/HAD-like	CATH (4.3.0)
B	3.40.50.1000	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	HAD superfamily/HAD-like	CATH (4.3.0)
A	3.40.50.1000	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	HAD superfamily/HAD-like	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF00702	haloacid dehalogenase-like hydrolase (Hydrolase)	haloacid dehalogenase-like hydrolase	This family is structurally different from the alpha/beta hydrolase family (Pfam:PF00561). This family includes L-2-haloacid dehalogenase, epoxide hydrolases and phosphatases. The structure of the family consists of two domains. One is an inserted fo ...	This family is structurally different from the alpha/beta hydrolase family (Pfam:PF00561). This family includes L-2-haloacid dehalogenase, epoxide hydrolases and phosphatases. The structure of the family consists of two domains. One is an inserted four helix bundle, which is the least well conserved region of the alignment, between residues 16 and 96 of Swiss:P24069. The rest of the fold is composed of the core alpha/beta domain [1]. Those members with the characteristic DxD triad at the N-terminus are probably phosphatidylglycerolphosphate (PGP) phosphatases involved in cardiolipin biosynthesis in the mitochondria [2].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	3-DEOXY-D-MANNO-OCTULOSONATE 8-PHOSPHATE PHOSPHATASE KDSC	phosphoric ester hydrolase activity 3-deoxy-manno-octulosonate-8-phosphatase activity hydrolase activity, acting on ester bonds phosphatase activity hydrolase activity catalytic activity N-acylneuraminate cytidylyltransferase activity cytidylyltransferase activity transferase activity nucleotidyltransferase activity transferase activity, transferring phosphorus-containing groups cation binding ion binding binding phosphoric ester hydrolase activity 3-deoxy-manno-octulosonate-8-phosphatase activity hydrolase activity, acting on ester bonds phosphatase activity hydrolase activity catalytic activity N-acylneuraminate cytidylyltransferase activity cytidylyltransferase activity transferase activity nucleotidyltransferase activity transferase activity, transferring phosphorus-containing groups cation binding ion binding binding metal ion binding small molecule binding	lipopolysaccharide biosynthetic process carbohydrate derivative biosynthetic process carbohydrate metabolic process polysaccharide biosynthetic process carbohydrate biosynthetic process liposaccharide metabolic process lipid biosynthetic process carbohydrate derivative metabolic process primary metabolic process macromolecule biosynthetic process lipopolysaccharide metabolic process polysaccharide metabolic process biosynthetic process metabolic process lipopolysaccharide biosynthetic process carbohydrate derivative biosynthetic process carbohydrate metabolic process polysaccharide biosynthetic process carbohydrate biosynthetic process liposaccharide metabolic process lipid biosynthetic process carbohydrate derivative metabolic process primary metabolic process macromolecule biosynthetic process lipopolysaccharide metabolic process polysaccharide metabolic process biosynthetic process metabolic process cellular process macromolecule metabolic process lipid metabolic process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR050793	CMP-NeuNAc synthase	Family
A, B, C, D	IPR036412	HAD-like superfamily	Homologous Superfamily
A, B, C, D	IPR023214	HAD superfamily	Homologous Superfamily
A, B, C, D	IPR010023	KdsC family	Family

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.